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. 2006 Jan 1;34(Database issue):D452-5.
doi: 10.1093/nar/gkj041.

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser

Kevin P Byrne  1 , Kenneth H Wolfe
Affiliations

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser

Kevin P Byrne et al. Nucleic Acids Res. .

Abstract

The Yeast Gene Order Browser (YGOB) is an online tool designed to facilitate the comparative genomic visualization and appraisal of synteny within and between the genomes of seven hemiascomycete yeast species. Three of these genomes are polyploid, and hence contain intra-genomic syntenic regions, the correct assembly of which is a particular success of YGOB. Designed to accurately assemble, display and score gene order relationships, YGOB is both an interactive tool for browsing genomic data, and a software engine now being used for evolutionary analyses on a whole-genome scale. Underlying the online interface is the YGOB database, which consists of homology assignments across the species, extensively curated based on sequence similarity and novelly, an appraisal of genomic context (synteny) in multiple genomes. Currently the YGOB database incorporates genome data from Saccharomyces cerevisiae, Candida glabrata, Saccharomyces castellii, Ashbya gossypii, Kluyveromyces lactis, Kluyveromyces waltii and Saccharomyces kluyveri, but the system is scaleable to accommodate additional genomes. This paper discusses the usage and utility of version 1.0 of YGOB, which is publicly available at http://wolfe.gen.tcd.ie/ygob.

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Figures

Figure 1
Figure 1
(A) Approximate phylogenetic relationship of the yeasts included in YGOB, with the WGD event marked as a closed circle. The tree is based on Kurtzman et al. (10). (B) YGOB screenshot focused on the A.gossypii gene AGL112C with a window size of 6. Tracks are labeled at right. At the bottom of the interface is the control console, which allows users to select the window size and the gene to focus on. Each box in the display represents a gene, and each color, a chromosome. The ‘b’ buttons open a window with BLASTP results against YGOB's database, ‘S’ buttons click through to protein sequences, ‘T’ buttons draw approximate phylogenetic trees and ‘+’ buttons output YGOB data in a tabulated text format.
Figure 2
Figure 2
YGOB bioinformatics utilities screenshots for the homology pillar containing the S.cerevisiae gene REF2, and labeled ‘c’ in Figure 1B. Clockwise from top left: (A) protein sequences for the pillar; (B) SGD and Gene Ontology information for REF2; (C) BLASTP results for Ref2 against the YGOB database; and (D) approximate phylogenetic tree for genes in the pillar.
See this image and copyright information in PMC

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